Jean knew. The revelations in Bendis run makes this scene make more sense
She did not get access to her TP until she was college aged, and she had been training directly with Profesor Xavier so she wasnt accidentally prying into people's thoughts. She didnt know when they were teenagers but she likely found out at any point when he allowed her into his head but decided to respect his privacy bc being gay wasnt as acceptable as it is now and it was a sensitive subject. Teen Jean had her TP forced onto her and she had no formal training when it happened. She was younger with far less experience and maturity and she was thrust into a world where homosexuality was more acceptable and in some ways celebrated. She also got to see the older Bobby continue to live his life in secret likely bc he never got the support and love that she felt she could give the teen version by letting him know she was there for him